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| Status |
Public on Oct 02, 2017 |
| Title |
Scrambled 1 rep 4 |
| Sample type |
SRA |
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| Source name |
lung tissue
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| Organism |
Mus musculus |
| Characteristics |
tissue: lung
strain: C57BL/6
age: post natal day 14
treatment: Scrambled 1 (10 mg/kg, P1,P3)
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| Treatment protocol |
Saline (daily treatment) group was treated via i.p. injection (25µl/g) daily from the postnatal day (P)1 to P13. Scramble antagomiR controls: Scrambled 1 (Custom miRCURY™ LNA Inhibitor probe, batch number 184196, Exiqon) and Scrambled 2 (Custom miRCURY™ LNA Inhibitor probe, New scramble control design, Exiqon) were applied at P1 and P3, by i.p. injection (10 mg/kg) dissolved in nuclease-Free Water (Ambion). Nuclease-Free Water (Ambion) was applied via i.p injection at P1 and P3 at (10µl/g). At P14 mice from Saline (daily treatment), Scrambled 1, Scrambled 2, Water and Untreated groups were sacrificed. Tamoxifen (Sigma-Aldrich) was applied at P1 and P2, by i.p. injection (0.4 mg; 25 µl) dissolved in Miglyol. Migloyl was applied at P1 and P2 at 25 µl via i.p. injection. Saline (treatment day 1+2) was applied at P1 and P2 at 25 µl via i.p. route. At P6 mice from Tamoxifen, Migloyl and Saline (treatment day 1+2) treatment groups were sacrificed.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were euthanized with pentobarbital for P6 or with isoflurane for P14. Thoracic cavity was opened and lungs were perfused through the heart with PBS. Lung were placed in RNAlater (Qiagen) overnight in 4°C and then transferred to -80°C. Lungs were homogenized with Precellys 24 homogenizer. Total RNA was extracted with peqGOLD Total RNA kit following the manufacturer’s instructions.
Library preparation was performed with the TruSeq Stranded mRNA HT technology High Sample (HS) according to the manufacturer´s protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
bcl2fastq 2.0 software tool was used for signal processing and demultiplexing
The RNA-Seq analysis was performed with the CLC Genomics Workbench V9.5.1 “RNA-Seq analysis” tool and mapped against the mouse reference genome (mmGRCm38.p3) to generate expression tables for every sample
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods, 2008. In short the value was calculated as follows: RPKM = total exon read count / mapped reads [millions] * exon length [kb]
Genome_build: mmGRCm38.p3
Supplementary_files_format_and_content: files are in csv format and contain the RPKM values
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| Submission date |
Dec 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Rory Morty |
| Organization name |
MPI für Herz- und Lungenforschung
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| Department |
W.G. Kerckhoff-Institut
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| Street address |
Parkstr. 1
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| City |
Bad Nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE92891 |
Impact of control interventions on lung gene expression in post-natal lung development |
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| Relations |
| BioSample |
SAMN06183484 |
| SRA |
SRX2443953 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2439384_16089-0025_S31_GE_.csv.gz |
2.2 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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